Trouble with negative frequencies


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Just Got Here
Yes, gladly. This is one of the submitted NWChem input files:
Example 1


echo
start Iso1_Cd1Se2
memory total 8000 mb
charge 1

#Iso1_Cd1Se2_2_B3LYP_cc-pVTZ-PP
geometry units angstrom noautoz noautosym
Cd    0.082077410000      1.420620500000     -1.402792040000
Se    0.413989940000     -0.953124550000     -0.044427640000
Se   -0.531980300000     -0.924193230000      1.918203620000
end

#  cc-pVTZ-PP  EMSL  Basis Set Exchange Library  12/31/17 9:22 AM
# Elements                             References
# --------                             ----------
# Ga-As,In-Sb, Tl-Bi   : K.A. Peterson, J. Chem. Phys. 119, 11099 (2003).
# Se-Kr, Te-Xe, Po-Rn  : K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
# M. Dolg, J. Chem. Phys. 119, 11113 (2003).
# Cu, Zn, Pd, Ag, Au, Hg: K.A. Peterson and C. Puzzarini, Theor. Chem. Acc., 114, 283 (2005)
# Y Zr Nb Mo Tc Ru Rh Pd     : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I    : K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
BASIS "ao basis" PRINT
#BASIS SET: (10s,11p,9d,1f) -> [5s,4p,3d,1f]
Se    S
   8991.8000000              0.0004210             -0.0001650        
   1355.2000000              0.0029330             -0.0011040        
    303.4980000              0.0098700             -0.0040150        
     44.3870000              0.0808600             -0.0276280        
     17.1581000             -0.3914900              0.1415820        
      3.5026200              0.6863270             -0.3316090        
      1.6158300              0.4855820             -0.3848760        
Se    S
      0.5046210              1.0000000        
Se    S
      0.2407280              1.0000000        
Se    S
      0.1025980              1.0000000        
Se    P
    491.8970000              0.0003680             -0.0001150        
     89.2328000              0.0048720             -0.0011020        
     25.5069000             -0.0885470              0.0230250        
      6.6999200              0.3466370             -0.1044220        
      3.1877200              0.5068780             -0.1640980        
      1.4838500              0.2515060             -0.0724090        
      0.5621350              0.0219950              0.3278190        
      0.2210550             -0.0012350              0.5611980        
      0.0822520              0.0006100              0.2784910        
Se    P
      0.6364000              1.0000000        
Se    P
      0.0978000              1.0000000        
Se    D
    301.8680000              0.0016370        
     92.1254000              0.0169670        
     37.9081000              0.0741760        
     16.4171000              0.1894830        
      7.4149600              0.3234940        
      3.3373800              0.3715420        
      1.4643800              0.2597780        
Se    D
      0.5825160              1.0000000        
Se    D
      0.2162000              1.0000000        
Se    F
      0.4696000              1.0000000        
#BASIS SET: (10s,9p,8d,2f,1g) -> [5s,5p,4d,2f,1g]
Cd    S
    257.4970000              0.0007680             -0.0002310              0.0004270              0.0014390        
     21.3546000             -0.0781940              0.0222790             -0.0241760             -0.1719290        
     13.4806000              0.4609280             -0.1382050              0.2190290              0.9499110        
      8.4865100             -0.5362100              0.1777840             -0.1984150             -1.5172470        
      5.3255100             -0.4008230              0.1056950             -0.5647670              0.1055120        
      1.6268600              0.8553620             -0.3259540              1.8215160              3.3939830        
      0.7404690              0.4898680             -0.2993250             -0.8098690             -4.0474090        
      0.1809330              0.0220290              0.2821000             -1.9098510              2.4869710        
      0.0850960             -0.0083600              0.6020440              1.4360880             -0.5824690        
Cd    S
      0.0363840              1.0000000        
Cd    P
    243.1650000              0.0001130             -0.0000370             -0.0000610             -0.0000860        
     13.9588000              0.0696720             -0.0165070             -0.0330520             -0.0719040        
      8.3100100             -0.2536750              0.0636620              0.1255300              0.2712270        
      2.2020000              0.4824920             -0.1465210             -0.3052730             -0.9039590        
      1.1007200              0.4845500             -0.1561870             -0.3223690             -0.2760210        
      0.5359750              0.1796400             -0.0273550              0.1819080              1.4946140        
      0.2136540              0.0152290              0.3226010              0.6863790             -0.2070140        
      0.0854690             -0.0001880              0.5566980              0.3216860             -0.7304040        
Cd    P
      0.0338230              1.0000000        
Cd    D
     86.0666000              0.0004430              0.0006330             -0.0003260        
     22.6386000              0.0050060              0.0073050             -0.0146770        
     12.1384000             -0.0160770             -0.0238720              0.0459900        
      3.4408100              0.1771520              0.3340440             -0.6525580        
      1.7176100              0.3666560              0.5448850             -0.2130730        
      0.8148490              0.3772260             -0.1745820              1.1468110        
      0.3660070              0.2339200             -0.6047310             -0.2158710        
Cd    D
      0.1502820              1.0000000        
Cd    F
      2.9086000              1.0000000        
Cd    F
      0.8508000              1.0000000        
Cd    G
      1.8019000              1.0000000        
END
# ELEMENTS                      REFERENCES
# ---------                       ----------
# O: B. Metz and H. Stoll, private communication (KAP)
# Tl: B. Metz, M. Schweizer, H. Stoll, M. Dolg, W. Liu, Theor. Chem. Acc. 104, 22 (2000).
# Ga-As, In-Sb, Pb-Bi: B. Metz, H. Stoll, M. Dolg, J. Chem. Phys. 113, 2563 (2000).
# Se-Kr, Te-Xe, Po-Rn: K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and M. Dolg, J. Chem. Phys., in press (2003).
# Cu, Zn, Ag, Cd, Au, Hg: D. Figgen, G. Rauhut, M. Dolg, and H. Stoll, Chem. Phys. 311, 227 (2005).
# Y Zr Nb Mo Tc Ru Rh Pd : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I: K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
ECP
Se nelec 10
Se ul
2      1.0000000              0.0000000        
Se S
2     30.0469900            370.1228880        
2      6.9186880             10.4561680        
Se P
2     45.7730140             99.1350590        
2     45.2946420            198.2924830        
2     20.7396480             28.3387470        
2     20.0286010             56.7497470        
Se D
2     50.9417680            -18.5265560        
2     49.5947400            -28.3349210        
2     16.3235220             -0.6960890        
2     14.4651960             -1.1678910        
2      3.7753300              0.0414430        
2      3.5019530              0.2355830        
Se F
2     11.9508670             -0.7662620        
2     17.8107800             -2.1027420        
Cd nelec 28
Cd ul
2      1.0000000              0.0000000        
Cd S
2     13.3551760            270.0394480        
2      7.3083780             38.8777660        
Cd P
2     12.6597280             64.6074700        
2     12.2896390            129.2194450        
2      6.7861760             10.6225580        
2      6.4007430             21.2650460        
Cd D
2     11.1617220             31.6639650        
2     11.2196150             47.4892160        
2      4.5377330              5.1862000        
2      4.3357270              7.5660630        
Cd F
2     11.4789860            -12.6327850        
2     11.4870270            -16.7601710        
END

#B3LYP
dft
 xc b3lyp
 direct
 grid xfine
 mult 2
 convergence ncydp 0 dampon 1d99 dampoff 1d-7 damp 70
 iterations 3000
 noio
end

driver
 xyz Iso1_Cd1Se2
 trust 0.3
 tight
 maxiter 200
end
     
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25              
task dft optimize
task dft frequencies


The resulting frequencies are:

----------------------------------------------------------------------------
Normal Eigenvalue || Projected Infra Red Intensities
Mode [cm**-1] || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
------ ---------- || -------------- ----------------- ---------- -----------
1 -272.983 || 0.000572 0.013 0.557 2.255
2 -136.209 || 0.002082 0.048 2.030 8.214
3 -0.000 || 0.000871 0.020 0.849 3.434
4 -0.000 || 0.001649 0.038 1.608 6.505
5 -0.000 || 0.003059 0.071 2.982 12.067
6 0.000 || 0.001711 0.039 1.668 6.751
7 0.000 || 0.003323 0.077 3.239 13.107
8 0.000 || 0.001331 0.031 1.297 5.249
9 161.271 || 0.008218 0.190 8.011 32.417
----------------------------------------------------------------------------

If I only switch the task dft frequencies to task dft frequencies numerical than all frequencies are positve:

----------------------------------------------------------------------------
Normal Eigenvalue ||           Projected Infra Red Intensities
Mode [cm**-1] || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
------ ---------- || -------------- ----------------- ---------- -----------
1 -0.000 || 0.000617 0.014 0.602 2.471
2 0.000 || 0.004188 0.097 4.083 16.771
3 0.000 || 0.002311 0.053 2.253 9.255
4 0.000 || 0.002829 0.065 2.758 11.329
5 0.000 || 0.000959 0.022 0.935 3.839
6 0.000 || 0.002369 0.055 2.310 9.488
7 69.530 || 0.000462 0.011 0.451 1.851
8 134.561 || 0.001121 0.026 1.093 4.488
9 368.364 || 0.007618 0.176 7.426 30.507
----------------------------------------------------------------------------




Example 2:

The following input file produces an even more strange result, because after geometry optimisation one obtains only negative frequencies:

echo
start Iso1_Se4
memory total 8000 mb
charge 1

#Iso1_Se4_2_PBE0_cc-pVTZ-PP
geometry units angstrom noautoz noautosym
Se   -0.473825546110      1.717840275589      1.028941993772
Se    0.000485660781     -0.845265976921     -1.029893516657
Se    1.180466149055     -1.332002348834      1.032100843165
Se   -0.707214508724      0.459516226371     -1.031237602320
end

#  cc-pVTZ-PP  EMSL  Basis Set Exchange Library  12/31/17 9:21 AM
# Elements                             References
# --------                             ----------
# Ga-As,In-Sb, Tl-Bi   : K.A. Peterson, J. Chem. Phys. 119, 11099 (2003).
# Se-Kr, Te-Xe, Po-Rn  : K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
# M. Dolg, J. Chem. Phys. 119, 11113 (2003).
# Cu, Zn, Pd, Ag, Au, Hg: K.A. Peterson and C. Puzzarini, Theor. Chem. Acc., 114, 283 (2005)
# Y Zr Nb Mo Tc Ru Rh Pd     : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I    : K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
BASIS "ao basis" PRINT
#BASIS SET: (10s,11p,9d,1f) -> [5s,4p,3d,1f]
Se    S
   8991.8000000              0.0004210             -0.0001650        
   1355.2000000              0.0029330             -0.0011040        
    303.4980000              0.0098700             -0.0040150        
     44.3870000              0.0808600             -0.0276280        
     17.1581000             -0.3914900              0.1415820        
      3.5026200              0.6863270             -0.3316090        
      1.6158300              0.4855820             -0.3848760        
Se    S
      0.5046210              1.0000000        
Se    S
      0.2407280              1.0000000        
Se    S
      0.1025980              1.0000000        
Se    P
    491.8970000              0.0003680             -0.0001150        
     89.2328000              0.0048720             -0.0011020        
     25.5069000             -0.0885470              0.0230250        
      6.6999200              0.3466370             -0.1044220        
      3.1877200              0.5068780             -0.1640980        
      1.4838500              0.2515060             -0.0724090        
      0.5621350              0.0219950              0.3278190        
      0.2210550             -0.0012350              0.5611980        
      0.0822520              0.0006100              0.2784910        
Se    P
      0.6364000              1.0000000        
Se    P
      0.0978000              1.0000000        
Se    D
    301.8680000              0.0016370        
     92.1254000              0.0169670        
     37.9081000              0.0741760        
     16.4171000              0.1894830        
      7.4149600              0.3234940        
      3.3373800              0.3715420        
      1.4643800              0.2597780        
Se    D
      0.5825160              1.0000000        
Se    D
      0.2162000              1.0000000        
Se    F
      0.4696000              1.0000000        
END
# ELEMENTS                      REFERENCES
# ---------                       ----------
# O: B. Metz and H. Stoll, private communication (KAP)
# Tl: B. Metz, M. Schweizer, H. Stoll, M. Dolg, W. Liu, Theor. Chem. Acc. 104, 22 (2000).
# Ga-As, In-Sb, Pb-Bi: B. Metz, H. Stoll, M. Dolg, J. Chem. Phys. 113, 2563 (2000).
# Se-Kr, Te-Xe, Po-Rn: K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and M. Dolg, J. Chem. Phys., in press (2003).
# Cu, Zn, Ag, Cd, Au, Hg: D. Figgen, G. Rauhut, M. Dolg, and H. Stoll, Chem. Phys. 311, 227 (2005).
# Y Zr Nb Mo Tc Ru Rh Pd : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I: K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
ECP
Se nelec 10
Se ul
2      1.0000000              0.0000000        
Se S
2     30.0469900            370.1228880        
2      6.9186880             10.4561680        
Se P
2     45.7730140             99.1350590        
2     45.2946420            198.2924830        
2     20.7396480             28.3387470        
2     20.0286010             56.7497470        
Se D
2     50.9417680            -18.5265560        
2     49.5947400            -28.3349210        
2     16.3235220             -0.6960890        
2     14.4651960             -1.1678910        
2      3.7753300              0.0414430        
2      3.5019530              0.2355830        
Se F
2     11.9508670             -0.7662620        
2     17.8107800             -2.1027420        
END

#PBE0
dft
 xc pbe0
 direct
 grid xfine
 mult 2
 convergence ncydp 0 dampon 1d99 dampoff 1d-7 damp 70
 iterations 3000
 noio
end

driver
 xyz Iso1_Se4
 trust 0.3
 tight
 maxiter 300
end
     
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25              
task dft optimize
task dft frequencies



The output frequencies are:

----------------------------------------------------------------------------
Normal Eigenvalue ||           Projected Infra Red Intensities
Mode [cm**-1] || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
------ ---------- || -------------- ----------------- ---------- -----------
1 -472.151 || 0.006800 0.157 6.629 37.931
2 -460.248 || 0.000000 0.000 0.000 0.000
3 -448.696 || 0.000000 0.000 0.000 0.000
4 -401.204 || 0.000000 0.000 0.000 0.000
5 -343.142 || 0.005197 0.120 5.066 28.986
6 -289.069 || 0.000000 0.000 0.000 0.000
7 -0.000 || 0.002430 0.056 2.369 13.557
8 -0.000 || 0.000273 0.006 0.266 1.520
9 -0.000 || 0.002348 0.054 2.289 13.099
10 -0.000 || 0.000810 0.019 0.789 4.516
11 -0.000 || 0.001915 0.044 1.867 10.681
12 0.000 || 0.001741 0.040 1.697 9.710
----------------------------------------------------------------------------

Again by performing a numerical frequency analysis, all frequencies are positive, which I would expect after a geometry optimisation.

Thank you in advance